Detailed view for LmjF.32.3930

Basic information

TDR Targets ID: 24046
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.5449 | Length (AA): 4087 | MW (Da): 454271 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG2

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00622   SPRY domain
PF00632   HECT-domain (ubiquitin-transferase)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0016881   acid-amino acid ligase activity  
GO:0008270   zinc ion binding  
GO:0005515   protein binding  
GO:0004842   ubiquitin-protein ligase activity  
GO:0006464   protein modification process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 22 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
287 381 2h14 (A) 40 131 20.00 0.00000004 0.16 0.2 -0.21
3548 3741 1q0u (A) 9 210 10.00 0 0.02 -0.03 -0.09
3563 3743 1wrb (A) 201 398 10.00 0 0.02 -0.03 -0.15
3717 4080 1zvd (A) 370 741 22.00 0 1 0.16 -0.75
243 367 4lg8 (A) 295 421 22.00 0.17 0.55 0.178985 0.01
269 614 3sfz (A) 633 981 19.00 0.00012 0.74 0.0620587 0.91
290 357 4nsx (A) 583 648 21.00 0.57 0.39 0.233038 -0.43
786 936 4me9 (A) 22 183 15.00 0 0.61 0.172546 -0.14
786 938 4kwa (A) 114 281 17.00 0 0.68 0.187036 -0.26
1193 1316 1d9s (A) 10 127 14.00 0.00000015 0.05 -0.0512599 0.91
1206 1316 1dcq (A) 406 504 12.00 0.00016 0.02 0.0295593 -0.16
1563 1686 2yyo (A) 33 162 18.00 0 0.55 0.0659401 -0.07
1569 1693 5ji7 (A) 214 337 33.00 0.0025 0.97 0.178385 0.1
1906 2050 2ihs (A) 89 228 16.00 0 0.26 0.213078 -0.66
1969 2045 4qt6 (A) 2108 2179 32.00 0.37 1 0.39064 -0.21
2466 2513 2n1a (B) 208 248 32.00 0.23 0.65 0.203145 0.08
2467 2517 2n1a (B) 209 251 37.00 0 0.51 0.227079 0
2519 2567 4i9x (A) 47 103 41.00 0.81 0.08 0.141789 1.19
3443 3579 4xw3 (A) 130 259 28.00 0.026 0.9 0.363321 -0.49
3444 3531 4p9i (A) 1099 1181 35.00 0.021 0.52 0.210332 0.24
3674 4081 3olm (A) 390 803 18.00 0.000000000078 1 0.200229 0.44
4001 4078 3pt3 (A) 2709 2791 32.00 0.00038 1 0.444485 -1.11

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile amastigotes. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_151799)

Species Accession Gene Product
Leishmania braziliensis LbrM.32.4170   hypothetical protein, conserved
Leishmania donovani LdBPK_324080.1   SPRY domain/HECT-domain (ubiquitin-transferase), putative
Leishmania infantum LinJ.32.4080   hypothetical protein, conserved
Leishmania major LmjF.32.3930   hypothetical protein, conserved
Leishmania mexicana LmxM.31.3930   hypothetical protein, conserved
Trypanosoma brucei gambiense Tbg972.11.18250   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.16260   SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma congolense TcIL3000_0_12400   SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma cruzi TcCLB.398751.10   SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma cruzi TcCLB.508525.60   SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma cruzi TcCLB.511527.9   SPRY domain/HECT-domain (ubiquitin-transferase), putative

Essentiality

LmjF.32.3930 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.7940 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.7940 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.7940 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.7940 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Druggability index (range: 0 to 1): 0.1

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier LmjF.32.3930 (Leishmania major), hypothetical protein, conserved
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